A number of genome-editing systems, such as designer zinc fingers, transcription activator-like effectors (TALEs), CRISPRs, and homing meganucleases, have been developed. One issue with these systems is that they require a both the identification of target sites for modification and the designing of a reagents specific for those sites, which is often laborious and time consuming. In one aspect, the invention allows for the efficient design, preparation, and use of genome editing reagents.